openPMD-api: 0.16.1+ (#5375)

Update to the latest stable release of openPMD-api, version 0.16.1.

Author: ax3l

.github/workflows/clang_tidy.yml

@@ -20,7 +20,7 @@ jobs:
         dim: [1, 2, RZ, 3]
     name: clang-tidy-${{ matrix.dim }}D
     runs-on: ubuntu-22.04
-    timeout-minutes: 180
+    timeout-minutes: 220
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v4

.github/workflows/cuda.yml

@@ -56,7 +56,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         cmake-easyinstall --prefix=/usr/local \
-          git+https://github.com/openPMD/openPMD-api.git@0.15.1 \
+          git+https://github.com/openPMD/openPMD-api.git@0.16.1 \
           -DopenPMD_USE_PYTHON=OFF    \
           -DBUILD_TESTING=OFF         \
           -DBUILD_EXAMPLES=OFF        \

.github/workflows/dependencies/icc.sh

@@ -58,7 +58,7 @@ export CEI_TMP="/tmp/cei"
 CXX=$(which icpc) CC=$(which icc) \
   cmake-easyinstall               \
   --prefix=/usr/local             \
-  git+https://github.com/openPMD/openPMD-api.git@0.15.2 \
+  git+https://github.com/openPMD/openPMD-api.git@0.16.1 \
   -DopenPMD_USE_PYTHON=OFF \
   -DBUILD_TESTING=OFF      \
   -DBUILD_EXAMPLES=OFF     \

Docs/source/developers/gnumake/openpmd.rst

@@ -9,7 +9,7 @@ therefore we recommend to use `spack <https://
 spack.io>`__ in order to facilitate the installation.
 
 More specifically, we recommend that you try installing the
-`openPMD-api library 0.15.1 or newer <https://openpmd-api.readthedocs.io/en/0.15.1/>`__
+`openPMD-api library 0.16.1 or newer <https://openpmd-api.readthedocs.io/en/0.16.1/>`__
 using spack (first section below). If this fails, a back-up solution
 is to install parallel HDF5 with spack, and then install the openPMD-api
 library from source.

Docs/source/install/cmake.rst

@@ -128,7 +128,7 @@ CMake Option                  Default & Values                               Des
 ``WarpX_amrex_internal``      **ON**/OFF                                     Needs a pre-installed AMReX library if set to ``OFF``
 ``WarpX_openpmd_src``         *None*                                         Path to openPMD-api source directory (preferred if set)
 ``WarpX_openpmd_repo``        ``https://github.com/openPMD/openPMD-api.git`` Repository URI to pull and build openPMD-api from
-``WarpX_openpmd_branch``      ``0.15.2``                                     Repository branch for ``WarpX_openpmd_repo``
+``WarpX_openpmd_branch``      ``0.16.1``                                     Repository branch for ``WarpX_openpmd_repo``
 ``WarpX_openpmd_internal``    **ON**/OFF                                     Needs a pre-installed openPMD-api library if set to ``OFF``
 ``WarpX_picsar_src``          *None*                                         Path to PICSAR source directory (preferred if set)
 ``WarpX_picsar_repo``         ``https://github.com/ECP-WarpX/picsar.git``    Repository URI to pull and build PICSAR from

Docs/source/install/dependencies.rst

@@ -30,7 +30,7 @@ Optional dependencies include:
   - also needs the ``pkg-config`` tool on Unix
 - `BLAS++ <https://github.com/icl-utk-edu/blaspp>`__ and `LAPACK++ <https://github.com/icl-utk-edu/lapackpp>`__: for spectral solver (PSATD) support in RZ geometry
 - `Boost 1.66.0+ <https://www.boost.org/>`__: for QED lookup tables generation support
-- `openPMD-api 0.15.1+ <https://github.com/openPMD/openPMD-api>`__: we automatically download and compile a copy of openPMD-api for openPMD I/O support
+- `openPMD-api 0.16.1+ <https://github.com/openPMD/openPMD-api>`__: we automatically download and compile a copy of openPMD-api for openPMD I/O support
 
   - see `optional I/O backends <https://github.com/openPMD/openPMD-api#dependencies>`__, i.e., ADIOS2 and/or HDF5
 - `Ascent 0.8.0+ <https://ascent.readthedocs.io>`__: for in situ 3D visualization

Docs/source/usage/parameters.rst

@@ -2780,18 +2780,18 @@ In-situ capabilities can be used by turning on Sensei or Ascent (provided they a
     When WarpX is compiled with openPMD support, the first available backend in the order given above is taken.
 
 * ``<diag_name>.openpmd_encoding`` (optional, ``v`` (variable based), ``f`` (file based) or ``g`` (group based) ) only read if ``<diag_name>.format = openpmd``.
-     openPMD `file output encoding <https://openpmd-api.readthedocs.io/en/0.15.2/usage/concepts.html#iteration-and-series>`__.
+     openPMD `file output encoding <https://openpmd-api.readthedocs.io/en/0.16.1/usage/concepts.html#iteration-and-series>`__.
      File based: one file per timestep (slower), group/variable based: one file for all steps (faster)).
-     ``variable based`` is an `experimental feature with ADIOS2 <https://openpmd-api.readthedocs.io/en/0.15.2/backends/adios2.html#experimental-new-adios2-schema>`__ and not supported for back-transformed diagnostics.
+     ``variable based`` is an `experimental feature with ADIOS2 <https://openpmd-api.readthedocs.io/en/0.16.1/backends/adios2.html#experimental-new-adios2-schema>`__ and not supported for back-transformed diagnostics.
      Default: ``f`` (full diagnostics)
 
 * ``<diag_name>.adios2_operator.type`` (``zfp``, ``blosc``) optional,
-    `ADIOS2 I/O operator type <https://openpmd-api.readthedocs.io/en/0.15.2/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
+    `ADIOS2 I/O operator type <https://openpmd-api.readthedocs.io/en/0.16.1/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
 
 * ``<diag_name>.adios2_operator.parameters.*`` optional,
-    `ADIOS2 I/O operator parameters <https://openpmd-api.readthedocs.io/en/0.15.2/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
+    `ADIOS2 I/O operator parameters <https://openpmd-api.readthedocs.io/en/0.16.1/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
 
-    A typical example for `ADIOS2 output using lossless compression <https://openpmd-api.readthedocs.io/en/0.15.2/details/backendconfig.html#adios2>`__ with ``blosc`` using the ``zstd`` compressor and 6 CPU treads per MPI Rank (e.g. for a `GPU run with spare CPU resources <https://arxiv.org/abs/1706.00522>`__):
+    A typical example for `ADIOS2 output using lossless compression <https://openpmd-api.readthedocs.io/en/0.16.1/details/backendconfig.html#adios2>`__ with ``blosc`` using the ``zstd`` compressor and 6 CPU treads per MPI Rank (e.g. for a `GPU run with spare CPU resources <https://arxiv.org/abs/1706.00522>`__):
 
     .. code-block:: text
 
@@ -2810,11 +2810,11 @@ In-situ capabilities can be used by turning on Sensei or Ascent (provided they a
         <diag_name>.adios2_operator.parameters.precision = 3
 
 * ``<diag_name>.adios2_engine.type`` (``bp4``, ``sst``, ``ssc``, ``dataman``) optional,
-    `ADIOS2 Engine type <https://openpmd-api.readthedocs.io/en/0.15.2/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
+    `ADIOS2 Engine type <https://openpmd-api.readthedocs.io/en/0.16.1/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
     See full list of engines at `ADIOS2 readthedocs <https://adios2.readthedocs.io/en/latest/engines/engines.html>`__
 
 * ``<diag_name>.adios2_engine.parameters.*`` optional,
-    `ADIOS2 Engine parameters <https://openpmd-api.readthedocs.io/en/0.15.2/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
+    `ADIOS2 Engine parameters <https://openpmd-api.readthedocs.io/en/0.16.1/details/backendconfig.html#adios2>`__ for `openPMD <https://www.openPMD.org>`_ data dumps.
 
     An example for parameters for the BP engine are setting the number of writers (``NumAggregators``), transparently redirecting data to burst buffers etc.
     A detailed list of engine-specific parameters are available at the official `ADIOS2 documentation <https://adios2.readthedocs.io/en/latest/engines/engines.html>`__

Source/Diagnostics/requirements.txt

@@ -5,4 +5,4 @@
 # License: BSD-3-Clause-LBNL
 
 # keep this entry for GitHub's dependency graph
-openPMD-api>=0.15.1
+openPMD-api>=0.16.1

Source/Make.WarpX

@@ -151,7 +151,7 @@ endif
 
 ifeq ($(USE_OPENPMD), TRUE)
   # try pkg-config query
-  ifeq (0, $(shell pkg-config "openPMD >= 0.15.1"; echo $$?))
+  ifeq (0, $(shell pkg-config "openPMD >= 0.16.1"; echo $$?))
     CXXFLAGS += $(shell pkg-config --cflags openPMD)
     LIBRARY_LOCATIONS += $(shell pkg-config --variable=libdir openPMD)
     libraries += $(shell pkg-config --libs-only-l openPMD)

Tools/machines/karolina-it4i/spack-karolina-cuda.yaml

@@ -20,7 +20,7 @@ spack:
   - py-cython
   - py-mpi4py
   - py-numpy@1.24.2
-  - openpmd-api@0.15.2 +python
+  - openpmd-api@0.16.1 +python
   - py-periodictable@1.5.0
   - py-h5py
 # optional

cmake/dependencies/openPMD.cmake

@@ -13,7 +13,7 @@ function(find_openpmd)
     if(WarpX_openpmd_internal OR WarpX_openpmd_src)
         set(CMAKE_POLICY_DEFAULT_CMP0077 NEW)
 
-        # see https://openpmd-api.readthedocs.io/en/0.15.2/dev/buildoptions.html
+        # see https://openpmd-api.readthedocs.io/en/0.16.1/dev/buildoptions.html
         set(openPMD_USE_ADIOS1      OFF           CACHE INTERNAL "")
         set(openPMD_USE_MPI         ${WarpX_MPI}  CACHE INTERNAL "")
         set(openPMD_USE_PYTHON      OFF           CACHE INTERNAL "")
@@ -71,7 +71,7 @@ function(find_openpmd)
         else()
             set(COMPONENT_WMPI NOMPI)
         endif()
-        find_package(openPMD 0.15.1 CONFIG REQUIRED COMPONENTS ${COMPONENT_WMPI})
+        find_package(openPMD 0.16.1 CONFIG REQUIRED COMPONENTS ${COMPONENT_WMPI})
         message(STATUS "openPMD-api: Found version '${openPMD_VERSION}'")
     endif()
 endfunction()
@@ -87,7 +87,7 @@ if(WarpX_OPENPMD)
     set(WarpX_openpmd_repo "https://github.com/openPMD/openPMD-api.git"
         CACHE STRING
         "Repository URI to pull and build openPMD-api from if(WarpX_openpmd_internal)")
-    set(WarpX_openpmd_branch "0.15.2"
+    set(WarpX_openpmd_branch "0.16.1"
         CACHE STRING
         "Repository branch for WarpX_openpmd_repo if(WarpX_openpmd_internal)")
 

setup.py

@@ -318,7 +318,7 @@ def build_extension(self, ext):
     # },
     extras_require={
         "all": [
-            "openPMD-api~=0.15.1",
+            "openPMD-api>=0.16.1",
             "openPMD-viewer~=1.1",
             "yt>=4.1.0",
             "matplotlib",